Molecular Genetics & Epigenomics (MGEL)

The Molecular Genetics and Epigenomics Laboratory Venu (Kal) Kalavacharla, Ph.D.
EPSCOR - Del State EPSCOR - Del State

Principal Investigator: Dr. Venugopal ‘Kal’ Kalavacharla

**If you have any questions or inquiries please send them HERE


The long-term goal is to improve legume crops for biotic and abiotic stresses. Currently we are leveraging the plant resources we have in common bean (Phaseolus vulgaris) to understand the resistance mechanisms exhibited by plants upon inoculation with a rust fungal pathogen called Uromyces appendiculatus.

Our current focus in the lab is the epigenetic analysis of common bean during the active fungal infection stage. We are trying to map DNA- protein interaction sites on the common bean and mung bean genomes through ChIP-sequencing and bioinformatics tools. Additionally we are also looking at epigenetic changes brought by modifications in methylation, histone acetylation, histone deacetylation and small RNAs.

Our 454-sequence analysis contributed a substantial number of common bean sequences to the GenBank public depository. This project also helped us find large number of resistance gene-like sequences (PvRGLs), and Simple Sequence Repeats (SSR) in common bean.

U. appendiculatus produces rust-like lesions called urediniospores on the leaf tissue providing rust-like appearance in the field, which may cause up to fifty percent yield loss in common bean. Previously we were able to identify the Ur-3 locus, which is responsible for disease resistance to 44 out of 89 rust races identified in the United States.  

The common bean genotype Sierra posses the Ur-3 locus and shows hypersensitive resistance  (HR) response to rust race 53. We also have three susceptible mutants developed from Sierra by fast neutron bombardment.   We were able to identify deletion region in the mutants that have changes in the Ur-3region of the genome using the Amplified Fragment Length Polymorphism (AFLPs) technique. 

Visitors and Researchers Link

Lab Demonstrations Link

MGEL Collaborators

Jyothi Thimmapuram – Bioinformatics Core, Purdue University, West Lafayette, Indiana

Malay Saha – The Samuel Roberts Noble Foundation Ardmore, Oklahoma

Muthusamy Manoharan – Department of Agriculture, University of Arkansas, Pine Bluff, Arkansas

Lab Members



Dr. Antonette Todd

Dr. Mayavan Subramani

Dr. Vasu Ayyappan


Graduate Students:

Ms. Rita K. Hayford

Mr. Rasheed Habib

Ms. Latoya Irvin

Ms. Miranda Penney

Mr. Nyasha Shumbayarerwa


Undergraduate Students:

Ms. Fedrica Williams

Ms. Lily Lofton

Ms. Ayiana James

Ms. Daniela Rivera


Past Members:

Ms. Mariama Brown

Ms. Elizabeth Fiedler

Mr. Isaac Fisher​

Mr. Staffon Nicholas

Ms. Josephine Veeria

Publications (Newest – Oldest)

Ayyappan, V., Sripathi, VR., Kalavacharla, V., Saha, MC., Thimmapuram, J., Bhide, KP. and Fiedler, E. Genome-wide identification of histone modifications in upland (AP13) and lowland (VS16) ecotypes of switchgrass. BMC Genomics. 20:687: 1-15. 2019.

Todd, A.R.; Donofrio, N.; Sripathi, V.R.; McClean, P.E.; Lee, R.K.; Pastor-Corrales, M.; Kalavacharla, V.K. (2017) Marker-Assisted Molecular Profiling, Deletion Mutant Analysis, and RNA-Seq Reveal a Disease Resistance Cluster Associated with Uromyces appendiculatus Infection in Common Bean Phaseolus vulgaris L.Int. J. Mol. Sci. 2017, 18, 1109.

Kalavacharla, V. (Kal), Subramani, M., Ayyappan, V., Dworkin, M. C., & Hayford, R. K. (2017). Plant Epigenomics. Handbook of Epigenetics, 245–258.

Dworkin, M., Xie, S., Saha, M., Thimmapuram, J., & Kalavacharla, V. K. (2017). Analyses of methylomes of upland and lowland switchgrass ( Panicum virgatum ) ecotypes using MeDIP-seq and BS-seq. BMC Genomics, 1–14.

Vasudevan, V., Subramanyam, K., Elayaraja, D., Karthik, S., Vasudevan, A., & Manickavasagam, M. (2017). Assessment of the efficacy of amino acids and polyamines on regeneration of watermelon (Citrullus lanatus Thunb.) and analysis of genetic fidelity of regenerated plants by SCoT and RAPD markersPlant Cell, Tissue and Organ Culture (PCTOC)130(3), 681-687.

Hayford, R. K., Ligaba-osena, A., Subramani, M., Melmaiee, K., Hossain, K., & Kalavacharla, V. K. (2017). Characterization and Expression Analysis of Common Bean Histone Deacetylase 6 during Development and Cold Stress Response. International Journal of Genomics2017, 12.

Ayyappan, V., Saha, M. C., Thimmapuram, J., Sripathi, V. R., Bhide, K. P., Fiedler, E., … Kalavacharla, V. K. (2016). Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass. Plant Cell Reports36(1), 1–22.

Crampton, M., Sripathi, V. R., Hossain, K., & Kalavacharla, V. (2016). Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing. Frontiers in Plant Science7(April), 447.

Melmaiee, K., Kalavacharla, V., Brown, A., Todd, A., Thurston, Y., & Elavarthi, S. (2015). Quantification and gene expression analysis of histone deacetylases in common bean during rust fungal inoculation. International Journal of Genomics.

Ayyappan, V., Kalavacharla, V., Thimmapuram, J., Bhide, K. P., Sripathi, V. R., Smolinski, T. G., … Mantovani, R. (2015). Genome-wide profiling of histone modifications and gene expression in rust (uromyces appendiculatus) inoculated common bean (Phaseolus vulgaris L). PLoS ONE10(7), 1–29.

Hickey, M. E., Besong, S. A., Kalavacharla, V., & Lee, J. L. (2013). Identification of extracellular DNase-producing bacterial populations on catfish fillets during refrigerated storage. Food Science and Biotechnology22(1), 87–92.

Melmaiee, K., Todd, A., Mcclean, P., Lee, R., Schlueter, J., Jackson, S., & Kalavacharla, V. (2013). Identification of molecular markers associated with the deleted region in common bean ( Phaseolus vulgaris ) ur-3 mutants. Australian Journal of Crop Science, 7(3), 354–360.

Liu, Z., Crampton, M., Todd, A., & Kalavacharla, V. (2012). Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.). BMC Plant Biology12(1), 42.

Kunjeti, S. G., Evans, T. A., Marsh, A. G., Gregory, N. F., Kunjeti, S., Meyers, B. C., Kalavacharla, V. S. and Donofrio, N. M. (2012), RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew. Molecular Plant Pathology, 13: 454–466. doi:10.1111/j.1364-3703.2011.00761.x

Kalavacharla, V., Liu, Z., Meyers, B. C., Thimmapuram, J., & Melmaiee, K. (2011). Identification and analysis of common bean ( Phaseolus vulgaris L .) transcriptomes by massively parallel pyrosequencing. BMC Plant Biology11(1), 135.

Liu, L., Yu, L., Kalavacharla, V., & Liu, Z. (2011). A Bayesian model for gene family evolution. BMC Bioinformatics12, 426.

Abebe, T., Melmaiee, K., Berg, V., & Wise, R. P. (2010). Drought response in the spikes of barley: Gene expression in the lemma, palea, awn, and seed. Functional and Integrative Genomics10(2), 191–205.

Michalak, M., Kumar, A., Gu, Y., Paux, E., Choulet, F., Feuillet, C., … Sf, K. (2008). High-resolution radiation hybrid mapping in wheat : an essential tool for the construction of the wheat physical maps, 7–9.

Kalavacharla, V., Hossain, K., Gu, Y., Riera-Lizarazu, O., Vales, M. I., Bhamidimarri, S., … Kianian, S. F. (2006). High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D. Genetics173(2), 1089–1099.

Kalavacharla, V., Hossain, K., Maan, S. S., Kianian, S. F. (2005). Nuclear cytoplasmic interactions in wheat. Recent Research Developments in Genetics and Breeding Vol 2: 71-84

Hossain, K. G., Kalavacharla, V., Lazo, G. R., Hegstad, J., Wentz, M. J., Kianian, P. M. A., … Kianian, S. F. (2004). A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7. Genetics168(2), 687–699.

Lazo, G. R., Chao, S., Hummel, D. D., Edwards, H., Crossman, C. C., Lui, N., … Anderson, O. D. (2004). Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.): EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map. Genetics168(2), 585–593.

Munkvold, J. D., Greene, R. A., Bermudez-Kandianis, C. E., La Rota, C. M., Edwards, H., Sorrells, S. F., … Sorrells, M. E. (2004). Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1. Genetics168(2), 639–650.

Hossain, K. G., Riera-Lizarazu, O., Kalavacharla, V., Vales, M. I., Maan, S. S., & Kianian, S. F. (2004). Radiation Hybrid Mapping of the Species Cytoplasm-Specific (scs(ae)) Gene in Wheat. Genetics168(1), 415–423.

Peng, J. H., Zadeh, H., Lazo, G. R., Gustafson, J. P., Chao, S., Anderson, O. D., … Lapitan, N. L. V. (2004). Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis. Genetics168(2), 609–623.

Randhawa, H. S., Dilbirligi, M., Sidhu, D., Erayman, M., Sandhu, D., Bondareva, S., … Gill, K. S. (2004). Deletion Mapping of Homoeologous Group 6-Specific Wheat Expressed Sequence Tags. Genetics168(2), 677–686.

Miftahudin, Ross, K., Ma, X.-F., Mahmoud, A. A., Layton, J., Milla, M. A. R., … Gustafson, J. P. (2004). Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4. Genetics168(2), 651–663.

Conley, E. J., Nduati, V., Gonzalez-Hernandez, J. L., Mesfin, A., Trudeau-Spanjers, M., Chao, S., … Anderson, J. A. (2004). A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice. Genetics168(2), 625–637.

Linkiewicz, A. M., Qi, L. L., Gill, B. S., Ratnasiri, A., Echalier, B., Chao, S., … Dubcovsky, J. (2004). A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With RiceGenetics168(2), 665–676.

Qi, L. L., Echalier, B., Chao, S., Lazo, G. R., Butler, G. E., Anderson, O. D., … Gill, B. S. (2004). A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat.Genetics168(2), 701–712.

Hossain, K. G., Riera-Lizarazu, O., Kalavacharla, V., Vales, M. I., Rust, J. L., Maan, S. S., & Kianian, S. F. (2004). Molecular cytogenetic characterization of an alloplasmic durum wheat line with a portion of chromosome 1D of Triticum aestivum carrying the scsae gene. Genome47(1), 206–214.

Sorrells, M. E., La Rota, M., Bermudez-Kandianis, C. E., Greene, R. A., Kantety, R., Munkvold, J. D., … Qualset. (2003). Comparative DNA Sequence Analysis of Wheat and Rice Genomes. Genome Research13(8), 1818–1827.

Akhunov, E. D., Goodyear, A. W., Geng, S., Qi, L.-L., Echalier, B., Gill, B. S., … Dvorak. (2003). The Organization and Rate of Evolution of Wheat Genomes Are Correlated With Recombination Rates Along Chromosome Arms. Genome Research13(5), 753–763.

Kianian, S.F., Hossain, K.G., Riera-Lizarazu, O., Kalavacharla, V.S., Vales, M.I and S.S. Maan. (2003). Radiation hybrid mapping of a species cytoplasm specific (scsae) gene in wheat. Proceedings of the Tenth International Wheat Genetics Symposium, 1-6 September, Italy, p. 597-597.

Gill, B.S., Qi, L., Echalier, B., Chao, S., Lazo, G.R., Anderson, O.D., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Dubcovsky, J., Bermidez-Kandianis, C.E., Greene, R.A., La Rota, M., Sorrells, M.E., Dilbirligi, M., Sidhu, D., Eryman, M., Gill, K.S., Miftahudin, Ma, X., Mahmoud, A., Gustafson, J.P., Wennerlind, E.J., Nduati, V., Gonzalez-Hernandez, L., Anderson, J.A., Peng, J., Lapitan, N.V., Hossain, K., Kalavacharla, V., Kianian, S.F., Pathan, M.S., Nguyen, H.T., Choi, D., Close, T.J., Mcguire, P.E., Qualset, C.O. (2003). A transcriptome map of wheat. In: Proceedings of the Wheat Genetics International Symposium, September 1-6. Paestum, Italy. p. 261-264.

Dvorak J, Akhunov ED, Akhunov AR, Luo M-C, Linkiewicz AM, Dubcovsky J, Hummel D, Lazo G, Chao S, Anderson OD, David J, Qi L, Echalier B, Gill BS, Miftahudin, Gustafson JP, La Rota M, Sorrells ME, Zhang D, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Wennerlind EJ, Nduati V, Anderson JA, Sidhu D, Gill KS, Choi D-W, Close TJ, McGuire PE, and Qualset CO. (2003). New insights into the organization and evolution of wheat genomes. 1:247-253.

Kalavacharla, V.S., Goreham, J., Spaeth, K., Osenga, M., Elias, E.M., Kianian, S.F. (2001). Progress towards saturation mapping and BAC contig development for Qfhs.NDSU-3AS a major FHB QTL in durum wheat. National Fusarium Head Blight Forum.

Kalavacharla, V., Stavely, J. R., Myers, J. R., & Mcclean, P. E. (2000). Crg , a Gene Required for Ur-3-Mediated Rust Resistance in Common Bean , Maps to a Resistance Gene Analog Cluster13(11), 1237–1242.

Kalavacharla, V.S., Wu, C., Rimmer, S. R. (1999). Genetic analysis for resistance to Albugo candida in Brassica differentials. In “New Horizons for an old crop” 10th International Rapeseed Congress.

Book Chapters​ (Newest – Oldest)

Venu (Kal) Kalavacharla, Mayavan Subramani, Vasudevan Ayyappan, Mollee C. Dworkin and Rita K. Hayford. (2017). Chapter 16 – Plant Epigenomics, In Handbook of Epigenetics (Second edition), edited by Trygve O. Tollefsbol, Academic Press, (pp. 245-258). ISBN 9780128053881. Preview Chapter>>

Melmaiee, K., & Kalavacharla, V. (2010). ESTs and their Role in Functional Genomics. In Principles and Practices of Plant Genomics, Volume 3 (pp. 104–119). Science Publishers.

Kalavacharla, V., Hossain, K., Riera-Lizarazu, O., Gu, Y., Maan, S. S., & Kianian, S. F. (2009). Chapter 6 Radiation Hybrid Mapping in Crop Plants. In B. T.-A. in Agronomy (Ed.) (Vol. Volume 102, pp. 201–222). Academic Press.

Kalavacharla VS., Hossain KG., Maan SS. and Kianian SF. (2005). Nuclear cytoplasmic interactions in wheat. Recent Res.Devel. Genet. Breeding, 2:71-84

Dr. Venu Kalavacharla

Department of Agriculture

And Natural Resources

Delaware State University

Dover, DE 19901

Phone: 302-857-6492


College of Agriculture, Science, and Technology